Identify mobile genetic elements present in genomic assemblies
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
fasta:file
FASTA file containing contigs/scaffolds/chromosomes
*.{fasta,fna,fa}
genomad_db:directory
Directory pointing to geNomad database
aggregated_classification
*_aggregated_classification/*_aggregated_classification.tsv:file
Combined classification scores for each contig/scaffold/chromosome
*_aggregated_classification.tsv
taxonomy
*_annotate/*_taxonomy.tsv:file
Detailed output of geNomad’s marker gene taxonomy analysis
*_taxonomy.tsv
provirus
*_find_proviruses/*_provirus.tsv:file
Detailed output of each provirus identified by geNomad’s find_proviruses module
*_provirus.tsv
compositions
*_score_calibration/*_compositions.tsv:file
OPTIONAL - Predicted sample composition when --enable-score-calibration is used
--enable-score-calibration
*_compositions.tsv
calibrated_classification
*_score_calibration/*_calibrated_aggregated_classification.tsv:file
OPTIONAL - Classification scores that have been adjusted based on sample composition when --enable-score-calibration is used`
*_calibrated_aggregated_classification.tsv
plasmid_fasta
*_summary/*_plasmid.fna.gz:file
FASTA file containing predicted plasmid sequences
*_plasmid.fna
plasmid_genes
*_summary/*_plasmid_genes.tsv:file
TSV file containing predicted plasmid genes and their annotations
*_plasmid_genes.tsv
plasmid_proteins
*_summary/*_plasmid_proteins.faa.gz:file
FASTA file containing predicted plasmid protein sequences
*_plasmid_proteins.faa
plasmid_summary
*_summary/*_plasmid_summary.tsv:file
TSV file containing a summary of geNomad’s plasmid predictions
*_plasmid_summary.tsv
virus_fasta
*_summary/*_virus.fna.gz:file
FASTA file containing predicted virus sequences
*_virus.fna
virus_genes
*_summary/*_virus_genes.tsv:file
TSV file containing predicted virus genes and their annotations
*_virus_genes.tsv
virus_proteins
*_summary/*_virus_proteins.faa.gz:file
FASTA file containing predicted virus protein sequences
*_virus_proteins.faa
virus_summary
*_summary/*_virus_summary.tsv:file
TSV file containing a summary of geNomad’s virus predictions
*_virus_summary.tsv
versions
versions.yml:file
File containing software versions
versions.yml
Identification of mobile genetic elements
